Graph accordance of next-generation sequence assemblies

Bioinformatics

Volumn 28, Issue 1, 2012, Pages 13-16

  Yao, Guohui ^a   Ye, Liang ^a   Gao, Hongyu ^a   Minx, Patrick ^a   Warren, Wesley C ^a   Weinstock, George M ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; CHICKEN; CONTIG MAPPING; DNA SEQUENCE; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; METHODOLOGY;

ALGORITHMS; ANIMALS; CHICKENS; CONTIG MAPPING; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA;

EID: 84855179453     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr588     Document Type: Article

References (18)

1. Alkan, C. et al. (2010) Limitations of next-generation genome sequence assembly. Nat. Methods, 8, 61-65.
2. Casagrande, A. et al. (2009) GAM: genomics assemblies merger: a graph based method to integrate different assemblies. In IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Washington, DC, pp. 321-326.
3. Consortium, I.C.G.S. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695-716.
4. DiGuistini, S. et al. (2009) De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol., 10, R94.
5. Gnerre, S. et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl Acad. Sci. USA, 108, 1513-1518.
6. Harismendy, O. et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol., 10, R32.
7. Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664
8. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
9. Li, R. et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature, 463, 311-317.
10. Margulies, M. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
11. Miller, J.R. et al. (2008) Aggressive assembly of pyrosequencing reads with mates. Bioinformatics, 24, 2818-2824.
12. Nagarajan, H. et al. (2010) De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads. PLoS One, 5, e10922.
13. Nijkamp, J. et al. (2010) Integrating genome assemblies with MAIA. Bioinformatics, 26, i433-i439.
14. Otto, T.D. et al. (2010) Iterative Correction of reference nucleotides (iCORN) using second generation sequencing Technology. Bioinformatics, 26, 1704-1707.
15. Simpson, J.T. et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
16. Surget-Groba, Y. and Montoya-Burgos, J.I. (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res., 20, 1432-1440.
17. Ye, L. et al. (2011) A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol., 12, R31.
18. Zimin, A.V. et al. (2008) Assembly reconciliation. Bioinformatics, 24, 42-45.